BLASTP 2.2.26 [Sep-21-2011]
Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer,
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997),
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs", Nucleic Acids Res. 25:3389-3402.
Reference for compositional score matrix adjustment: Altschul, Stephen F.,
John C. Wootton, E. Michael Gertz, Richa Agarwala, Aleksandr Morgulis,
Alejandro A. Schaffer, and Yi-Kuo Yu (2005) "Protein database searches
using compositionally adjusted substitution matrices", FEBS J. 272:5101-5109.
Query= 033799
(111 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1U96|A Chain A, Solution Structure Of Yeast Cox17 With Copper Bound
pdb|1U97|A Chain A, Solution Structure Of Apo Yeast Cox17
pdb|1Z2G|A Chain A, Solution Structure Of Apo, Oxidized Yeast Cox17
Length = 69
Score = 26.9 bits (58), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 13/32 (40%), Positives = 19/32 (59%)
Query: 31 CDLEKKDYIGCLKSSGHQSENCRIFSKKYLEC 62
C EK++ C+ +G SE C+ F +KY EC
Sbjct: 26 CKPEKEERDTCILFNGQDSEKCKEFIEKYKEC 57
>pdb|4GZY|D Chain D, Crystal Structures Of Bacterial Rna Polymerase Paused
Elongation Complexes
pdb|4GZZ|D Chain D, Crystal Structures Of Bacterial Rna Polymerase Paused
Elongation Complexes
Length = 1534
Score = 25.8 bits (55), Expect = 6.5, Method: Composition-based stats.
Identities = 18/68 (26%), Positives = 28/68 (41%), Gaps = 9/68 (13%)
Query: 22 VFPLDHMHQCDLEKKDYIGCLKSSGHQSENCRIFSKKYLECRMAKNAQSMHSLVHWERDN 81
V P +HQC L K+ + K KK E +A N ++ ++ +RD
Sbjct: 633 VGPQLKLHQCGLPKRMALELFKP---------FLLKKMEEKGIAPNVKAARRMLERQRDI 683
Query: 82 KGTIWALL 89
K +W L
Sbjct: 684 KDEVWDAL 691
>pdb|1IW7|D Chain D, Crystal Structure Of The Rna Polymerase Holoenzyme From
Thermus Thermophilus At 2.6a Resolution
pdb|1IW7|N Chain N, Crystal Structure Of The Rna Polymerase Holoenzyme From
Thermus Thermophilus At 2.6a Resolution
pdb|1SMY|D Chain D, Structural Basis For Transcription Regulation By Alarmone
Ppgpp
pdb|1SMY|N Chain N, Structural Basis For Transcription Regulation By Alarmone
Ppgpp
pdb|1ZYR|D Chain D, Structure Of Thermus Thermophilus Rna Polymerase
Holoenzyme In Complex With The Antibiotic Streptolydigin
pdb|1ZYR|N Chain N, Structure Of Thermus Thermophilus Rna Polymerase
Holoenzyme In Complex With The Antibiotic Streptolydigin
pdb|2A68|D Chain D, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme In Complex With Antibiotic Rifabutin
pdb|2A68|N Chain N, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme In Complex With Antibiotic Rifabutin
pdb|2A69|D Chain D, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme In Complex With Antibiotic Rifapentin
pdb|2A69|N Chain N, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme In Complex With Antibiotic Rifapentin
pdb|2A6E|D Chain D, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme
pdb|2A6E|N Chain N, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme
pdb|2A6H|D Chain D, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme In Complex With Antibiotic Sterptolydigin
pdb|2A6H|N Chain N, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme In Complex With Antibiotic Sterptolydigin
pdb|2CW0|D Chain D, Crystal Structure Of Thermus Thermophilus Rna Polymerase
Holoenzyme At 3.3 Angstroms Resolution
pdb|2CW0|N Chain N, Crystal Structure Of Thermus Thermophilus Rna Polymerase
Holoenzyme At 3.3 Angstroms Resolution
pdb|2BE5|D Chain D, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme In Complex With Inhibitor Tagetitoxin
pdb|2BE5|N Chain N, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme In Complex With Inhibitor Tagetitoxin
pdb|2O5I|D Chain D, Crystal Structure Of The T. Thermophilus Rna Polymerase
Elongation Complex
pdb|2O5I|N Chain N, Crystal Structure Of The T. Thermophilus Rna Polymerase
Elongation Complex
pdb|2O5J|D Chain D, Crystal Structure Of The T. Thermophilus Rnap Polymerase
Elongation Complex With The Ntp Substrate Analog
pdb|2O5J|N Chain N, Crystal Structure Of The T. Thermophilus Rnap Polymerase
Elongation Complex With The Ntp Substrate Analog
pdb|2PPB|D Chain D, Crystal Structure Of The T. Thermophilus Rnap Polymerase
Elongation Complex With The Ntp Substrate Analog And
Antibiotic Streptolydigin
pdb|2PPB|N Chain N, Crystal Structure Of The T. Thermophilus Rnap Polymerase
Elongation Complex With The Ntp Substrate Analog And
Antibiotic Streptolydigin
pdb|3DXJ|D Chain D, Crystal Structure Of Thermus Thermophilus Rna Polymerase
Holoenzyme In Complex With The Antibiotic Myxopyronin
pdb|3DXJ|N Chain N, Crystal Structure Of Thermus Thermophilus Rna Polymerase
Holoenzyme In Complex With The Antibiotic Myxopyronin
pdb|3EQL|D Chain D, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme In Complex With Antibiotic Myxopyronin
pdb|3EQL|N Chain N, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme In Complex With Antibiotic Myxopyronin
pdb|3AOH|D Chain D, Rna Polymerase-Gfh1 Complex (Crystal Type 1)
pdb|3AOH|I Chain I, Rna Polymerase-Gfh1 Complex (Crystal Type 1)
pdb|3AOH|N Chain N, Rna Polymerase-Gfh1 Complex (Crystal Type 1)
pdb|3AOI|D Chain D, Rna Polymerase-Gfh1 Complex (Crystal Type 2)
pdb|3AOI|I Chain I, Rna Polymerase-Gfh1 Complex (Crystal Type 2)
pdb|3AOI|N Chain N, Rna Polymerase-Gfh1 Complex (Crystal Type 2)
pdb|4G7H|D Chain D, Crystal Structure Of Thermus Thermophilus Transcription
Initiation Complex
pdb|4G7H|N Chain N, Crystal Structure Of Thermus Thermophilus Transcription
Initiation Complex
pdb|4G7O|D Chain D, Crystal Structure Of Thermus Thermophilus Transcription
Initiation Complex Containing 2 Nt Of Rna
pdb|4G7O|N Chain N, Crystal Structure Of Thermus Thermophilus Transcription
Initiation Complex Containing 2 Nt Of Rna
pdb|4G7Z|D Chain D, Crystal Structure Of Thermus Thermophilus Transcription
Initiation Complex Containing 5-Bru At Template-Strand
Position +1
pdb|4G7Z|N Chain N, Crystal Structure Of Thermus Thermophilus Transcription
Initiation Complex Containing 5-Bru At Template-Strand
Position +1
Length = 1524
Score = 25.8 bits (55), Expect = 6.5, Method: Composition-based stats.
Identities = 18/68 (26%), Positives = 28/68 (41%), Gaps = 9/68 (13%)
Query: 22 VFPLDHMHQCDLEKKDYIGCLKSSGHQSENCRIFSKKYLECRMAKNAQSMHSLVHWERDN 81
V P +HQC L K+ + K KK E +A N ++ ++ +RD
Sbjct: 633 VGPQLKLHQCGLPKRMALELFKP---------FLLKKMEEKGIAPNVKAARRMLERQRDI 683
Query: 82 KGTIWALL 89
K +W L
Sbjct: 684 KDEVWDAL 691
>pdb|1L9U|D Chain D, Thermus Aquaticus Rna Polymerase Holoenzyme At 4 A
Resolution
pdb|1L9U|M Chain M, Thermus Aquaticus Rna Polymerase Holoenzyme At 4 A
Resolution
pdb|1L9Z|D Chain D, Thermus Aquaticus Rna Polymerase HoloenzymeFORK-Junction
Promoter Dna Complex At 6.5 A Resolution
pdb|1YNJ|D Chain D, Taq Rna Polymerase-Sorangicin Complex
pdb|1YNJ|J Chain J, Taq Rna Polymerase-Sorangicin Complex
pdb|1YNN|D Chain D, Taq Rna Polymerase-rifampicin Complex
pdb|1YNN|J Chain J, Taq Rna Polymerase-rifampicin Complex
Length = 1524
Score = 25.8 bits (55), Expect = 7.0, Method: Composition-based stats.
Identities = 18/68 (26%), Positives = 27/68 (39%), Gaps = 9/68 (13%)
Query: 22 VFPLDHMHQCDLEKKDYIGCLKSSGHQSENCRIFSKKYLECRMAKNAQSMHSLVHWERDN 81
V P +HQC L K+ + K KK E A N ++ ++ +RD
Sbjct: 633 VGPQLKLHQCGLPKRMALELFKP---------FLLKKMEEKAFAPNVKAARRMLERQRDI 683
Query: 82 KGTIWALL 89
K +W L
Sbjct: 684 KDEVWDAL 691
>pdb|1I6V|D Chain D, Thermus Aquaticus Core Rna Polymerase-Rifampicin Complex
Length = 1264
Score = 25.8 bits (55), Expect = 7.0, Method: Composition-based stats.
Identities = 18/68 (26%), Positives = 27/68 (39%), Gaps = 9/68 (13%)
Query: 22 VFPLDHMHQCDLEKKDYIGCLKSSGHQSENCRIFSKKYLECRMAKNAQSMHSLVHWERDN 81
V P +HQC L K+ + K KK E A N ++ ++ +RD
Sbjct: 373 VGPQLKLHQCGLPKRMALELFKP---------FLLKKMEEKAFAPNVKAARRMLERQRDI 423
Query: 82 KGTIWALL 89
K +W L
Sbjct: 424 KDEVWDAL 431
>pdb|1HQM|D Chain D, Crystal Structure Of Thermus Aquaticus Core Rna
Polymerase- Includes Complete Structure With Side-Chains
(Except For Disordered Regions)-Further Refined From
Original Deposition-Contains Additional Sequence
Information
Length = 1265
Score = 25.8 bits (55), Expect = 7.0, Method: Composition-based stats.
Identities = 18/68 (26%), Positives = 27/68 (39%), Gaps = 9/68 (13%)
Query: 22 VFPLDHMHQCDLEKKDYIGCLKSSGHQSENCRIFSKKYLECRMAKNAQSMHSLVHWERDN 81
V P +HQC L K+ + K KK E A N ++ ++ +RD
Sbjct: 373 VGPQLKLHQCGLPKRMALELFKP---------FLLKKMEEKAFAPNVKAARRMLERQRDI 423
Query: 82 KGTIWALL 89
K +W L
Sbjct: 424 KDEVWDAL 431
>pdb|2GHO|D Chain D, Recombinant Thermus Aquaticus Rna Polymerase For
Structural Studies
Length = 1233
Score = 25.8 bits (55), Expect = 7.0, Method: Composition-based stats.
Identities = 18/68 (26%), Positives = 27/68 (39%), Gaps = 9/68 (13%)
Query: 22 VFPLDHMHQCDLEKKDYIGCLKSSGHQSENCRIFSKKYLECRMAKNAQSMHSLVHWERDN 81
V P +HQC L K+ + K KK E A N ++ ++ +RD
Sbjct: 342 VGPQLKLHQCGLPKRMALELFKP---------FLLKKMEEKAFAPNVKAARRMLERQRDI 392
Query: 82 KGTIWALL 89
K +W L
Sbjct: 393 KDEVWDAL 400
Database: pdbaa
Posted date: Mar 3, 2013 10:34 PM
Number of letters in database: 14,973,337
Number of sequences in database: 62,578
Lambda K H
0.323 0.135 0.438
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,094,077
Number of Sequences: 62578
Number of extensions: 105271
Number of successful extensions: 222
Number of sequences better than 100.0: 9
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 8
Number of HSP's that attempted gapping in prelim test: 221
Number of HSP's gapped (non-prelim): 9
length of query: 111
length of database: 14,973,337
effective HSP length: 75
effective length of query: 36
effective length of database: 10,279,987
effective search space: 370079532
effective search space used: 370079532
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 45 (21.9 bits)